With our overall design in mind, we must design DNA sequences, down to the base level, which undergo the interactions that we desire, without forming secondary structures and binding in unintended ways. We approach this through a combination of pre-generated noninteracting sequences, and trial-and-error design using NUPACK simulation software.

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==Sequence Level Design==

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Also, Random walking playground and cargo sorting playground were designed using a rectangular orgiami.

With our overall design in mind, we must design DNA sequences, down to the base level, which undergo the interactions that we desire, without forming secondary structures and binding in unintended ways. We approach this through a combination of pre-generated noninteracting sequences, and trial-and-error design using NUPACK simulation software.

We used three different experimental techniques, and here is the design of each experiments.

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== Experimental Design==

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1. Before constructing our origami and observing how it behaves, we run a large number of experiments observable through Gel Electrophoresis to verify that many of our mechanisms behave as we expect them to.

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=== Verification of Mechanisms through Gel Experiments===

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2. Various DNA strands are tagged with fluorophores and quenchers in order to investigate different mechanisms more directly, both in solution and on origami.

Before constructing our origami and observing how it behaves, we run a large number of experiments observable through Gel Electrophoresis to verify that many of our mechanisms behave as we expect them to.

With our overall design in mind, we must design DNA sequences, down to the base level, which undergo the interactions that we desire, without forming secondary structures and binding in unintended ways. We approach this through a combination of pre-generated noninteracting sequences, and trial-and-error design using NUPACK simulation software.

Also, Random walking playground and cargo sorting playground were designed using a rectangular orgiami.

Design of the experiments

We used three different experimental techniques, and here is the design of each experiments.

1. Before constructing our origami and observing how it behaves, we run a large number of experiments observable through Gel Electrophoresis to verify that many of our mechanisms behave as we expect them to.

2. Various DNA strands are tagged with fluorophores and quenchers in order to investigate different mechanisms more directly, both in solution and on origami.